YIAV - ECOLI - GREMLIN Contacts

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YIAV - Inner membrane protein YiaV

UniProt:	P37683	Sequences: MDLLIILTYVAFAWAMFKIFKIPVNKWTIPTAALGGIFIVSGLILLMNYNHPYTFKAQKAVISIPVVPQVTGVVIEVTDKKNTLIKKGEVLFRLDPTRYQARVDRLMADIVTAEHKQRALGAELDEMAANTQQAKATRDKFAKEYQRYARGSQAKVNPFSERDIDVARQNYLAQEASVKSSAAEQKQIQSQLDSLVLGEHSQIASLKAQLAEAKYNLEQTIVRAPSDGYVTQVLIRPGTYAASLPLRPVMVFIPDQKRQIVAQFRQNSLLRLAPGDDAEVVFNALPGKVFSGKLAAISPAVPGGAYQSTGTLQTLNTAPGSDGVIATIELDEHTDLSALPDGIYAQVAVYSDHFSHVSVMRKVLLRMTSWVHYLYLDH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12290
Length:	378 (318)
Sequences:	18055 (14352)
Seq/√Len:	804.8

ECOLI - YIAV YIBH EMRK EMRA YHII YBHG MDTN MACA ACRE AAEA ACRA YDHJ MDTA MDTE CUSB
BACSU - YVRP YKNX

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_E	93_R	3.375	1.00
86_K	227_D	3.255	1.00
90_V	221_I	3.075	1.00
295_A	329_E	2.738	1.00
292_G	328_I	2.588	1.00
142_A	146_Q	2.487	1.00
107_M	214_K	2.442	1.00
168_R	172_L	2.395	1.00
149_A	168_R	2.385	1.00
93_R	221_I	2.383	1.00
277_D	291_S	2.335	1.00
86_K	89_E	2.328	1.00
78_T	93_R	2.323	1.00
148_Y	159_F	2.302	1.00
96_P	100_Q	2.215	1.00
103_V	210_L	2.170	1.00
148_Y	167_A	2.163	1.00
142_A	175_E	2.128	1.00
149_A	155_K	2.124	1.00
90_V	223_R	2.103	1.00
114_E	207_K	2.038	1.00
69_Q	219_Q	2.031	1.00
84_L	229_Y	2.018	1.00
171_Y	175_E	2.017	1.00
87_K	227_D	2.007	1.00
78_T	90_V	1.968	1.00
138_R	171_Y	1.954	1.00
145_Y	164_I	1.876	1.00
261_V	325_I	1.874	1.00
161_E	165_D	1.869	1.00
142_A	171_Y	1.842	1.00
231_T	253_I	1.841	1.00
293_K	331_D	1.833	1.00
140_K	144_E	1.830	1.00
279_E	289_V	1.826	1.00
163_D	166_V	1.821	1.00
277_D	293_K	1.819	1.00
145_Y	149_A	1.813	1.00
135_K	182_A	1.808	1.00
103_V	214_K	1.806	1.00
279_E	291_S	1.802	1.00
259_Q	327_T	1.792	1.00
293_K	329_E	1.776	1.00
278_A	328_I	1.731	1.00
104_D	107_M	1.702	1.00
154_A	164_I	1.699	1.00
110_I	210_L	1.686	1.00
262_A	347_V	1.679	1.00
145_Y	171_Y	1.657	1.00
80_K	83_T	1.646	1.00
138_R	142_A	1.633	1.00
100_Q	217_L	1.620	1.00
204_A	207_K	1.594	1.00
103_V	107_M	1.591	1.00
296_A	327_T	1.584	1.00
262_A	328_I	1.568	1.00
135_K	178_V	1.567	1.00
105_R	209_Q	1.532	1.00
211_A	214_K	1.530	1.00
100_Q	104_D	1.524	1.00
224_A	252_F	1.520	1.00
40_V	44_I	1.519	1.00
102_R	105_R	1.517	1.00
139_D	143_K	1.515	1.00
60_A	261_V	1.511	1.00
164_I	168_R	1.507	1.00
111_V	114_E	1.505	1.00
138_R	175_E	1.498	1.00
175_E	179_K	1.489	1.00
72_G	94_L	1.487	1.00
125_D	128_A	1.478	1.00
260_I	345_A	1.477	1.00
107_M	210_L	1.476	1.00
145_Y	168_R	1.476	1.00
132_Q	135_K	1.473	1.00
92_F	222_V	1.470	1.00
84_L	255_D	1.468	1.00
75_I	95_D	1.467	1.00
110_I	114_E	1.454	1.00
172_L	175_E	1.435	1.00
110_I	207_K	1.412	1.00
131_T	178_V	1.404	1.00
74_V	235_I	1.402	1.00
118_R	121_G	1.391	1.00
128_A	189_Q	1.382	1.00
138_R	178_V	1.376	1.00
166_V	170_N	1.374	1.00
301_V	324_V	1.373	1.00
212_E	216_N	1.365	1.00
74_V	92_F	1.364	1.00
179_K	182_A	1.361	1.00
147_R	165_D	1.360	1.00
154_A	161_E	1.358	1.00
75_I	93_R	1.357	1.00
39_I	43_L	1.355	1.00
178_V	182_A	1.335	1.00
102_R	212_E	1.315	1.00
170_N	173_A	1.309	1.00
146_Q	150_R	1.304	1.00
144_E	166_V	1.294	1.00
197_L	200_H	1.291	1.00
110_I	203_I	1.290	1.00
279_E	350_Y	1.290	1.00
257_K	329_E	1.289	1.00
207_K	211_A	1.284	1.00
103_V	217_L	1.284	1.00
242_A	247_R	1.275	1.00
214_K	218_E	1.271	1.00
141_F	174_Q	1.269	1.00
137_T	173_A	1.266	1.00
186_K	189_Q	1.266	1.00
90_V	93_R	1.265	1.00
210_L	214_K	1.258	1.00
288_K	338_A	1.257	1.00
128_A	185_Q	1.257	1.00
41_S	44_I	1.254	1.00
146_Q	149_A	1.252	1.00
76_E	237_P	1.250	1.00
230_V	250_M	1.248	1.00
91_L	250_M	1.246	1.00
135_K	139_D	1.238	1.00
282_F	345_A	1.232	1.00
99_Y	220_T	1.230	1.00
162_R	166_V	1.209	1.00
41_S	45_L	1.207	1.00
265_R	268_S	1.205	1.00
139_D	142_A	1.198	1.00
149_A	164_I	1.183	1.00
102_R	216_N	1.172	1.00
65_P	248_P	1.162	1.00
83_T	89_E	1.159	1.00
40_V	43_L	1.157	1.00
291_S	331_D	1.154	1.00
79_D	89_E	1.152	1.00
150_R	156_V	1.151	1.00
215_Y	219_Q	1.148	1.00
165_D	168_R	1.138	1.00
59_K	260_I	1.136	1.00
264_F	272_L	1.135	1.00
96_P	220_T	1.123	1.00
228_G	252_F	1.119	1.00
130_N	133_Q	1.112	1.00
105_R	109_D	1.111	1.00
131_T	185_Q	1.106	1.00
202_Q	205_S	1.105	1.00
261_V	327_T	1.103	1.00
107_M	111_V	1.103	1.00
133_Q	177_S	1.100	1.00
279_E	348_A	1.096	1.00
294_L	326_A	1.081	1.00
144_E	162_R	1.073	1.00
63_S	251_V	1.072	1.00
272_L	349_V	1.069	1.00
185_Q	189_Q	1.066	1.00
143_K	165_D	1.065	1.00
281_V	348_A	1.065	1.00
64_I	226_S	1.064	1.00
264_F	326_A	1.064	1.00
68_P	222_V	1.063	1.00
272_L	294_L	1.062	1.00
38_F	42_G	1.059	1.00
109_D	112_T	1.057	1.00
109_D	205_S	1.049	1.00
65_P	251_V	1.049	1.00
131_T	135_K	1.046	1.00
170_N	174_Q	1.040	1.00
134_A	174_Q	1.028	1.00
241_A	249_V	1.027	1.00
121_G	196_V	1.026	1.00
81_K	232_Q	1.026	1.00
114_E	203_I	1.020	1.00
29_I	33_A	1.015	1.00
37_I	41_S	1.013	1.00
232_Q	251_V	1.013	1.00
334_T	338_A	1.012	1.00
200_H	204_A	1.004	1.00
280_V	330_L	0.998	1.00
198_G	202_Q	0.996	1.00
104_D	211_A	0.994	1.00
137_T	140_K	0.991	1.00
92_F	249_V	0.990	1.00
27_W	31_T	0.989	1.00
281_V	289_V	0.988	1.00
177_S	180_S	0.988	1.00
84_L	227_D	0.988	1.00
71_T	243_S	0.986	1.00
131_T	182_A	0.983	1.00
121_G	200_H	0.981	1.00
106_L	206_L	0.974	1.00
263_Q	325_I	0.965	1.00
139_D	172_L	0.964	1.00
233_V	236_R	0.962	1.00
77_V	237_P	0.962	1.00
224_A	227_D	0.962	1.00
128_A	132_Q	0.960	1.00
79_D	250_M	0.952	1.00
150_R	155_K	0.951	1.00
108_A	208_A	0.943	1.00
80_K	233_V	0.941	1.00
273_A	276_D	0.938	1.00
144_E	148_Y	0.927	1.00
116_K	202_Q	0.926	1.00
69_Q	73_V	0.924	1.00
117_Q	121_G	0.922	1.00
298_S	325_I	0.921	1.00
77_V	92_F	0.920	1.00
143_K	146_Q	0.917	1.00
62_I	254_P	0.916	1.00
350_Y	353_H	0.913	1.00
184_E	187_Q	0.912	1.00
203_I	207_K	0.906	1.00
73_V	240_Y	0.903	1.00
112_T	202_Q	0.896	1.00
113_A	206_L	0.896	1.00
57_A	260_I	0.895	1.00
124_L	189_Q	0.894	1.00
209_Q	212_E	0.893	1.00
254_P	257_K	0.891	1.00
159_F	163_D	0.884	1.00
116_K	119_A	0.881	1.00
68_P	241_A	0.881	1.00
264_F	349_V	0.876	1.00
148_Y	163_D	0.873	1.00
260_I	280_V	0.871	1.00
137_T	177_S	0.870	1.00
119_A	195_L	0.869	1.00
133_Q	137_T	0.867	1.00
101_A	215_Y	0.866	1.00
134_A	137_T	0.863	1.00
124_L	128_A	0.861	1.00
92_F	250_M	0.861	1.00
196_V	200_H	0.860	1.00
260_I	347_V	0.860	1.00
97_T	215_Y	0.853	1.00
215_Y	218_E	0.849	1.00
102_R	106_L	0.847	1.00
140_K	169_Q	0.846	1.00
101_A	208_A	0.845	1.00
71_T	242_A	0.843	1.00
233_V	250_M	0.842	1.00
173_A	177_S	0.839	1.00
294_L	328_I	0.838	1.00
103_V	213_A	0.838	1.00
85_I	91_L	0.838	1.00
93_R	96_P	0.836	1.00
167_A	170_N	0.835	1.00
74_V	241_A	0.832	1.00
99_Y	213_A	0.831	1.00
130_N	180_S	0.828	1.00
33_A	37_I	0.823	1.00
57_A	61_V	0.822	1.00
106_L	213_A	0.818	1.00
280_V	292_G	0.817	1.00
168_R	171_Y	0.816	1.00
109_D	113_A	0.811	1.00
205_S	209_Q	0.806	1.00
174_Q	177_S	0.803	1.00
282_F	285_L	0.802	1.00
195_L	198_G	0.798	1.00
285_L	290_F	0.797	1.00
259_Q	295_A	0.794	1.00
137_T	170_N	0.794	1.00
263_Q	323_G	0.792	1.00
117_Q	200_H	0.792	1.00
213_A	216_N	0.790	1.00
354_F	357_V	0.789	1.00
75_I	96_P	0.788	1.00
25_N	29_I	0.788	1.00
140_K	166_V	0.787	1.00
269_L	324_V	0.785	1.00
183_A	186_K	0.785	1.00
102_R	213_A	0.785	1.00
75_I	78_T	0.783	1.00
109_D	209_Q	0.778	1.00
157_N	161_E	0.776	1.00
134_A	181_S	0.776	1.00
280_V	345_A	0.774	1.00
62_I	236_R	0.773	1.00
112_T	116_K	0.772	1.00
68_P	249_V	0.760	1.00
127_M	130_N	0.760	1.00
130_N	184_E	0.756	1.00
66_V	250_M	0.752	1.00
218_E	223_R	0.752	1.00
278_A	292_G	0.749	1.00
79_D	230_V	0.749	1.00
122_A	125_D	0.748	1.00
123_E	187_Q	0.747	1.00
206_L	209_Q	0.747	1.00
199_E	203_I	0.747	1.00
71_T	240_Y	0.747	1.00
274_P	297_I	0.746	1.00
87_K	225_P	0.740	1.00
137_T	141_F	0.739	1.00
96_P	221_I	0.739	1.00
26_K	41_S	0.738	1.00
111_V	204_A	0.737	1.00
130_N	134_A	0.736	1.00
26_K	37_I	0.736	1.00
137_T	174_Q	0.732	1.00
159_F	164_I	0.732	1.00
26_K	30_P	0.731	1.00
154_A	159_F	0.729	1.00
277_D	350_Y	0.727	1.00
187_Q	191_Q	0.725	1.00
208_A	211_A	0.723	1.00
163_D	167_A	0.723	1.00
222_V	249_V	0.722	1.00
148_Y	162_R	0.721	1.00
66_V	225_P	0.718	1.00
106_L	109_D	0.715	1.00
134_A	177_S	0.715	1.00
226_S	252_F	0.715	1.00
36_G	40_V	0.714	1.00
199_E	202_Q	0.712	1.00
206_L	210_L	0.710	1.00
182_A	186_K	0.709	1.00
281_V	287_G	0.708	1.00
113_A	116_K	0.707	1.00
202_Q	206_L	0.706	1.00
234_L	251_V	0.706	1.00
186_K	190_S	0.697	1.00
281_V	346_Q	0.696	1.00
78_T	89_E	0.695	1.00
126_E	130_N	0.690	1.00
69_Q	98_R	0.689	1.00
114_E	118_R	0.688	1.00
180_S	184_E	0.683	1.00
73_V	95_D	0.683	1.00
141_F	170_N	0.682	1.00
61_V	341_D	0.681	1.00
284_A	343_I	0.678	1.00
169_Q	173_A	0.677	1.00
140_K	143_K	0.676	1.00
70_V	216_N	0.675	1.00
79_D	83_T	0.674	1.00
127_M	131_T	0.672	1.00
107_M	110_I	0.671	1.00
174_Q	178_V	0.671	1.00
302_P	325_I	0.670	1.00
161_E	164_I	0.664	1.00
28_T	32_A	0.662	1.00
54_T	346_Q	0.662	1.00
98_R	216_N	0.656	1.00
324_V	343_I	0.656	1.00
24_V	27_W	0.654	1.00
123_E	126_E	0.652	1.00
126_E	184_E	0.652	1.00
301_V	322_D	0.645	1.00
117_Q	203_I	0.643	1.00
189_Q	193_D	0.642	1.00
39_I	42_G	0.642	1.00
286_P	290_F	0.640	1.00
303_G	322_D	0.637	1.00
266_Q	344_Y	0.636	1.00
340_P	343_I	0.636	1.00
332_E	337_S	0.636	1.00
132_Q	136_A	0.636	1.00
59_K	258_R	0.635	1.00
96_P	217_L	0.635	1.00
99_Y	216_N	0.634	1.00
113_A	117_Q	0.634	1.00
113_A	199_E	0.632	1.00
259_Q	329_E	0.631	1.00
46_L	49_Y	0.630	1.00
101_A	104_D	0.627	1.00
98_R	102_R	0.627	1.00
160_S	163_D	0.619	1.00
229_Y	255_D	0.619	1.00
79_D	233_V	0.618	1.00
127_M	181_S	0.617	1.00
217_L	220_T	0.616	1.00
27_W	30_P	0.613	1.00
262_A	349_V	0.613	1.00
274_P	295_A	0.613	1.00
181_S	184_E	0.612	1.00
285_L	288_K	0.612	1.00
295_A	327_T	0.612	1.00
31_T	38_F	0.612	1.00
262_A	326_A	0.606	1.00
184_E	188_I	0.606	1.00
176_A	179_K	0.606	1.00
43_L	357_V	0.604	1.00
181_S	185_Q	0.603	1.00
141_F	167_A	0.601	1.00
134_A	178_V	0.599	1.00
100_Q	103_V	0.599	1.00
81_K	233_V	0.598	1.00
106_L	110_I	0.597	1.00
123_E	191_Q	0.597	1.00
68_P	71_T	0.596	1.00
258_R	341_D	0.596	1.00
216_N	219_Q	0.595	1.00
92_F	233_V	0.594	1.00
49_Y	52_P	0.594	1.00
67_V	240_Y	0.593	1.00
280_V	347_V	0.593	1.00
25_N	28_T	0.592	1.00
207_K	210_L	0.588	1.00
68_P	92_F	0.587	1.00
61_V	253_I	0.587	1.00
131_T	181_S	0.585	1.00
280_V	328_I	0.584	1.00
283_N	346_Q	0.583	1.00
129_A	132_Q	0.582	1.00
106_L	210_L	0.582	1.00
42_G	46_L	0.582	1.00
122_A	190_S	0.582	1.00
38_F	41_S	0.580	1.00
59_K	339_L	0.580	1.00
58_Q	261_V	0.580	1.00
26_K	29_I	0.579	1.00
123_E	127_M	0.577	1.00
276_D	351_S	0.577	1.00
105_R	212_E	0.577	1.00
124_L	185_Q	0.576	1.00
190_S	193_D	0.576	1.00
141_F	144_E	0.573	1.00
144_E	167_A	0.573	1.00
97_T	218_E	0.573	1.00
218_E	221_I	0.566	1.00
195_L	199_E	0.565	1.00
248_P	251_V	0.562	1.00
88_G	223_R	0.560	1.00
47_M	50_N	0.560	1.00
136_A	139_D	0.559	1.00
177_S	181_S	0.557	1.00
275_G	293_K	0.557	1.00
54_T	348_A	0.555	1.00
140_K	165_D	0.554	1.00
328_I	347_V	0.548	1.00
110_I	206_L	0.547	1.00
161_E	168_R	0.546	1.00
201_S	204_A	0.546	1.00
138_R	174_Q	0.546	1.00
242_A	246_L	0.545	1.00
285_L	343_I	0.542	1.00
253_I	341_D	0.542	1.00
175_E	178_V	0.541	1.00
98_R	215_Y	0.540	1.00
143_K	161_E	0.540	1.00
99_Y	217_L	0.538	1.00
213_A	217_L	0.537	1.00
99_Y	103_V	0.537	1.00
109_D	202_Q	0.536	1.00
112_T	115_H	0.536	1.00
85_I	224_A	0.534	1.00
70_V	219_Q	0.534	1.00
194_S	198_G	0.533	1.00
81_K	327_T	0.532	1.00
111_V	115_H	0.531	1.00
124_L	188_I	0.530	1.00
64_I	252_F	0.530	1.00
45_L	48_N	0.528	1.00
135_K	138_R	0.528	1.00
65_P	239_T	0.527	1.00
146_Q	171_Y	0.527	1.00
234_L	248_P	0.527	1.00
136_A	140_K	0.525	1.00
179_K	183_A	0.525	1.00
282_F	339_L	0.525	1.00
24_V	28_T	0.522	1.00
109_D	206_L	0.521	1.00
197_L	201_S	0.520	1.00
147_R	162_R	0.517	1.00
55_F	59_K	0.517	1.00
200_H	203_I	0.516	1.00
120_L	196_V	0.514	1.00
264_F	347_V	0.512	1.00
162_R	165_D	0.512	1.00
108_A	201_S	0.508	1.00
57_A	345_A	0.507	1.00
188_I	191_Q	0.507	1.00
260_I	330_L	0.506	1.00
165_D	169_Q	0.505	1.00
30_P	34_L	0.503	1.00
64_I	68_P	0.500	1.00

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4tkoB	1	0.7407	100	0.365	Contact Map
4dk0A	5	0.7593	100	0.379	Contact Map
3fppA	3	0.6958	100	0.39	Contact Map
2f1mA	2	0.6138	100	0.426	Contact Map
3lnnA	6	0.7831	100	0.432	Contact Map
1vf7A	5	0.5952	100	0.456	Contact Map
4l8jA	2	0.7011	100	0.459	Contact Map
3ne5B	3	0.6296	100	0.481	Contact Map
4kkuA	1	0.537	100	0.525	Contact Map
2k32A	1	0.3042	99.8	0.701	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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